Job ID = 16439000 SRX = SRX15206440 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:21:43 prefetch.2.10.7: 1) Downloading 'SRR19139371'... 2022-08-02T05:21:43 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:22:01 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:22:02 prefetch.2.10.7: 'SRR19139371' is valid 2022-08-02T05:22:02 prefetch.2.10.7: 1) 'SRR19139371' was downloaded successfully 2022-08-02T05:22:02 prefetch.2.10.7: 'SRR19139371' has 0 unresolved dependencies Read 10272998 spots for SRR19139371/SRR19139371.sra Written 10272998 spots for SRR19139371/SRR19139371.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439138 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:26 10272998 reads; of these: 10272998 (100.00%) were unpaired; of these: 352666 (3.43%) aligned 0 times 8423059 (81.99%) aligned exactly 1 time 1497273 (14.57%) aligned >1 times 96.57% overall alignment rate Time searching: 00:04:26 Overall time: 00:04:26 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 487715 / 9920332 = 0.0492 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 14:30:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206440/SRX15206440.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206440/SRX15206440.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206440/SRX15206440.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206440/SRX15206440.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 02 Aug 2022 14:30:15: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:30:15: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:30:21: 1000000 INFO @ Tue, 02 Aug 2022 14:30:28: 2000000 INFO @ Tue, 02 Aug 2022 14:30:34: 3000000 INFO @ Tue, 02 Aug 2022 14:30:40: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 14:30:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206440/SRX15206440.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206440/SRX15206440.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206440/SRX15206440.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206440/SRX15206440.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 02 Aug 2022 14:30:43: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:30:43: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:30:46: 5000000 INFO @ Tue, 02 Aug 2022 14:30:50: 1000000 INFO @ Tue, 02 Aug 2022 14:30:52: 6000000 INFO @ Tue, 02 Aug 2022 14:30:57: 2000000 INFO @ Tue, 02 Aug 2022 14:30:58: 7000000 INFO @ Tue, 02 Aug 2022 14:31:03: 8000000 INFO @ Tue, 02 Aug 2022 14:31:04: 3000000 INFO @ Tue, 02 Aug 2022 14:31:09: 9000000 INFO @ Tue, 02 Aug 2022 14:31:11: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 14:31:12: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:31:12: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:31:12: #1 total tags in treatment: 9432617 INFO @ Tue, 02 Aug 2022 14:31:12: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:31:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:31:12: #1 tags after filtering in treatment: 9432617 INFO @ Tue, 02 Aug 2022 14:31:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:31:12: #1 finished! INFO @ Tue, 02 Aug 2022 14:31:12: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:31:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:31:13: #2 number of paired peaks: 110 WARNING @ Tue, 02 Aug 2022 14:31:13: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Tue, 02 Aug 2022 14:31:13: start model_add_line... INFO @ Tue, 02 Aug 2022 14:31:13: start X-correlation... INFO @ Tue, 02 Aug 2022 14:31:13: end of X-cor INFO @ Tue, 02 Aug 2022 14:31:13: #2 finished! INFO @ Tue, 02 Aug 2022 14:31:13: #2 predicted fragment length is 170 bps INFO @ Tue, 02 Aug 2022 14:31:13: #2 alternative fragment length(s) may be 3,98,106,111,133,170,554,576 bps INFO @ Tue, 02 Aug 2022 14:31:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206440/SRX15206440.05_model.r INFO @ Tue, 02 Aug 2022 14:31:13: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:31:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:31:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206440/SRX15206440.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206440/SRX15206440.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206440/SRX15206440.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206440/SRX15206440.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 02 Aug 2022 14:31:13: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:31:13: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:31:17: 5000000 INFO @ Tue, 02 Aug 2022 14:31:20: 1000000 INFO @ Tue, 02 Aug 2022 14:31:24: 6000000 INFO @ Tue, 02 Aug 2022 14:31:27: 2000000 INFO @ Tue, 02 Aug 2022 14:31:30: 7000000 INFO @ Tue, 02 Aug 2022 14:31:31: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:31:34: 3000000 INFO @ Tue, 02 Aug 2022 14:31:36: 8000000 INFO @ Tue, 02 Aug 2022 14:31:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206440/SRX15206440.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:31:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206440/SRX15206440.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:31:41: 4000000 INFO @ Tue, 02 Aug 2022 14:31:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206440/SRX15206440.05_summits.bed INFO @ Tue, 02 Aug 2022 14:31:41: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (127 records, 4 fields): 33 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:31:42: 9000000 INFO @ Tue, 02 Aug 2022 14:31:45: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:31:45: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:31:45: #1 total tags in treatment: 9432617 INFO @ Tue, 02 Aug 2022 14:31:45: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:31:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:31:45: #1 tags after filtering in treatment: 9432617 INFO @ Tue, 02 Aug 2022 14:31:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:31:45: #1 finished! INFO @ Tue, 02 Aug 2022 14:31:45: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:31:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:31:46: #2 number of paired peaks: 110 WARNING @ Tue, 02 Aug 2022 14:31:46: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Tue, 02 Aug 2022 14:31:46: start model_add_line... INFO @ Tue, 02 Aug 2022 14:31:46: start X-correlation... INFO @ Tue, 02 Aug 2022 14:31:46: end of X-cor INFO @ Tue, 02 Aug 2022 14:31:46: #2 finished! INFO @ Tue, 02 Aug 2022 14:31:46: #2 predicted fragment length is 170 bps INFO @ Tue, 02 Aug 2022 14:31:46: #2 alternative fragment length(s) may be 3,98,106,111,133,170,554,576 bps INFO @ Tue, 02 Aug 2022 14:31:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206440/SRX15206440.10_model.r INFO @ Tue, 02 Aug 2022 14:31:46: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:31:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:31:48: 5000000 INFO @ Tue, 02 Aug 2022 14:31:55: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:32:01: 7000000 INFO @ Tue, 02 Aug 2022 14:32:05: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:32:07: 8000000 INFO @ Tue, 02 Aug 2022 14:32:14: 9000000 INFO @ Tue, 02 Aug 2022 14:32:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206440/SRX15206440.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:32:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206440/SRX15206440.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:32:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206440/SRX15206440.10_summits.bed INFO @ Tue, 02 Aug 2022 14:32:15: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (60 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:32:16: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:32:16: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:32:16: #1 total tags in treatment: 9432617 INFO @ Tue, 02 Aug 2022 14:32:16: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:32:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:32:16: #1 tags after filtering in treatment: 9432617 INFO @ Tue, 02 Aug 2022 14:32:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:32:16: #1 finished! INFO @ Tue, 02 Aug 2022 14:32:16: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:32:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:32:17: #2 number of paired peaks: 110 WARNING @ Tue, 02 Aug 2022 14:32:17: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Tue, 02 Aug 2022 14:32:17: start model_add_line... INFO @ Tue, 02 Aug 2022 14:32:17: start X-correlation... INFO @ Tue, 02 Aug 2022 14:32:17: end of X-cor INFO @ Tue, 02 Aug 2022 14:32:17: #2 finished! INFO @ Tue, 02 Aug 2022 14:32:17: #2 predicted fragment length is 170 bps INFO @ Tue, 02 Aug 2022 14:32:17: #2 alternative fragment length(s) may be 3,98,106,111,133,170,554,576 bps INFO @ Tue, 02 Aug 2022 14:32:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206440/SRX15206440.20_model.r INFO @ Tue, 02 Aug 2022 14:32:17: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:32:17: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:32:36: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:32:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206440/SRX15206440.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:32:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206440/SRX15206440.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:32:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206440/SRX15206440.20_summits.bed INFO @ Tue, 02 Aug 2022 14:32:46: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (20 records, 4 fields): 28 millis CompletedMACS2peakCalling